POST /supplement

Get the raw text of a paper's supplementary materials, an annotation of the methodological details included in them (which might not exist in the methods section), the context in which they are mentioned in the main text, and mapping of each supplementary material mentioned in the text to specific files within the directory of supplementary materials attached to the paper.

Input: DOI or a PDF of a scientific paper.

Request

Content-Type: multipart/form-data

Accepted keys: doi and file

JSON Body (if using DOI):

{
  "doi": "10.1038/s41592-020-01005-z"
}

JSON Body (if uploading a PDF):

file: "path_to_file.pdf"

Note: If both a doi and a file key are present in the request, the API uses the file key by default.

Response

{
  "doi": "10.3390/ijms22031484",
  "paper_input_type": "doi,
  "pdf_url": "https"//url.to-download-openaccess.paper/pdf",
  "archive_download_url": "https://url.to-download.supplementary/materials",
  "pmcid": "PMC7867340",
  "supplementary_files": [
    {
      "label": "12859_2024_5739_Fig1_HTML.jpg",
      "isDirectory": false
    },
    {
      // more supplementary files if they exist
    },
  ],
  "supplementary_materials_legends": [
    {
      "id": "Additional file 1: Fig. S1",
      "title": "RMSD values of Cell4D particle and bulk diffusion across multiple timescales.",
      "body": "RMSD values of Cell4D particle and bulk diffusion across multiple timescales.",
      "full_legend_text": "Additional file 1: Fig. S1. RMSD values of Cell4D particle and bulk diffusion across multiple timescales."
    },   
    {
      // 
    }   
  ],
  "supplement_methodological_details": [
    {
      "id": "Additional file 8",
      "context": "Text providing full details of the System and Methods, including cooperative binding kinetics, spatial organization arrangements, CEACAM1 activation model compartments, and discussion on empirical benefit.",
      "isMethodsRelevant": true,
      "processedContent": {
        "status": "processed",
        "sourceFilename": "12859_2024_5739_MOESM8_ESM.docx",
        "extractedData": {
          "content": [
            {
              "category": "Software",
              "methodological_item_name": "Cell4D Simulation Software",
              "description": "Cell4D is a general purpose spatial stochastic simulator for cellular pathways, written in C++. Currently, it does not support the use of multiple threads or multiple CPUs."
            },
            {
              "category": "ModelDetail",
              "methodological_item_name": "Cell4D Data Model Layers",
              "description": "Cell4D models contain mandatory layers: Environmental Variables (dimensions, time/space scale, time-cycles), Species Types (base molecules), Compartments (spatial coordinates, diffusion regions), Species (molecules/complexes, states, number, positions), Reactions (reactants, products, kinetics, spatial limits), and an optional Events layer (time/condition triggers, molecule addition/removal/transport)."
            },
            {
              "category": "Configuration",
              "methodological_item_name": "Cell4D Random Number Seed",
              "description": "A random number seed is used to initialize the simulation. It can be generated automatically or provided by the user to allow recapitulation of a simulation."
            },
            {
              "category": "Algorithm",
              "methodological_item_name": "Cell4D Deterministic Diffusion (Small Molecules)",
              "description": "For small molecules represented by local concentrations within a lattice cell (c-voxel), diffusion into neighboring c-voxels is calculated deterministically based on Fick's law."
            },
          ]
        }
      },
      "otherCandidateFiles": []
    },
  ],
  "supplement_context":  {
    "Additional file 8": "Text document providing full details of the Cell4D system and methods, including specific details on the Calmodulin activation and CEACAM1 activation systems, cooperative binding kinetics, and the spatial arrangements investigated for calcium release. Also referenced in the context of the level of detail needed for empirical benefit.",
    "Additional file 1: Fig. S1": "Figure referenced in the Results section on diffusion and reaction events, showing RMSD values for Cell4D particle and bulk diffusion across multiple timescales, supporting the accurate modeling of Brownian motion.",
    "Additional file 2: Fig. S2": "Figure referenced in the Results section on diffusion and reaction events, showing RMSD for Cell4D bulk molecule and particle diffusion across space scales, supporting the accurate modeling of Brownian motion across scales.",
    "Additional file 3: Fig. S3": "Figure referenced in the Results section on diffusion and reaction events, showing reaction products from unimolecular and two-particle bimolecular reactions over time. Fig. S3B specifically highlights the sensitivity of point-particle bimolecular reactions to timescale and reaction rate. Used in benchmarking reaction modeling.",
    "Additional file 4: Fig. S4": "Figure referenced in the Results section on diffusion and reaction events, summarizing bimolecular products over time for bulk-particle reactions using a Smoluchowski-based method, showing accuracy increases with diffusion rate. Used in benchmarking reaction modeling.",
    "Additional file 5: Fig. S5": "Figure referenced in the Results section on diffusion and reaction events, summarizing two-particle bimolecular products over time using the Andrews-Bray adjusted Smoluchowski method, demonstrating correction of errors seen without the adjustment. Used in benchmarking reaction modeling.",
    "Additional file 6: Fig. S6": "Figure referenced in the Results section on Calmodulin activation, showing saturation of calmodulin under varying calcium concentrations in well-mixed or microdomain conditions, supporting the finding of low activated calmodulin proportion under standard T cell activation Ca2+ levels in initial simulations.",
    "Additional file 7: Fig. S7": "Figure referenced in the Discussion section regarding CEACAM1 clustering, comparing surface CEACAM1 clustering in both the raft and no-raft Cell4D model variants, showing counter-intuitive results about total membrane localization.",
    "https://github.com/ParkinsonLab/cell4d": "Link to the project GitHub site, referenced in the Discussion section as providing \"movies\" as examples of Cell4D simulation visualizations, enhancing user understanding.",
  },
  "supplement_to_file_mapping": [
    {
      "id": "Additional file 8",
      "context": "Text document providing full details of the Cell4D system and methods, including specific details on the Calmodulin activation and CEACAM1 activation systems, cooperative binding kinetics, and the spatial arrangements investigated for calcium release. Also referenced in the context of the level of detail needed for empirical benefit.",
      "candidateFiles": [
        {
          "label": "12859_2024_5739_MOESM8_ESM.docx",
          "type": "document"
        }
      ]
    },
    {
      "id": "Additional file 1: Fig. S1",
      "context": "Figure referenced in the Results section on diffusion and reaction events, showing RMSD values for Cell4D particle and bulk diffusion across multiple timescales, supporting the accurate modeling of Brownian motion.",
      "candidateFiles": [
        {
          "label": "12859_2024_5739_MOESM1_ESM.pdf",
          "type": "pdf"
        },
      ],
    },
  ],
}